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Nucleic Acids Research 2006 34(Web Server issue):W463-W465; doi:10.1093/nar/gkl255
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1

Ming Zhang1,2, Anne-Kathrin Schultz1, Charles Calef2, Carla Kuiken2, Thomas Leitner2, Bette Korber2,3, Burkhard Morgenstern1 and Mario Stanke1,*

1 Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik Goldschmidtstraße 1, 37077 Göttingen, Germany 2 Theoretical Division, Los Alamos National Laboratory Los Alamos, NM 87545, USA 3 The Santa Fe Institute Santa Fe, NM 87501, USA

*To whom correspondence should be addressed. Tel: +1 831 459 5232; Fax: +1 831 459 1809

Received February 14, 2006. Revised March 2, 2006. Accepted March 30, 2006.

Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach proposed by Spang et al. The input data for our server is a partial or complete genome sequence from HIV-1; our tool assigns regions of the input sequence to known subtypes of HIV-1 and predicts phylogenetic breakpoints. jpHMM is available online at http://jphmm.gobics.de/.


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A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, and M. Stanke
jpHMM: Improving the reliability of recombination prediction in HIV-1
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W647 - W651.
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